If you have the Boatbuilding with Plywood book it talks about the battens either notched or floating. As far as the side frames touching the planking it's not a problem as long as they are fair. They can touch the planking and be glued to it. You just don't want to put a bunch of screws into the fra...

Keeping it as low as possible is a good idea. Mine went onto the trailer immediately and I never bothered to take the wheels off because I needed to move it around. Lower sure would have been nice when fairing the deck framing.

For the most part, a 1/2" or 3/8" asymmetry isn't going to matter a whole lot in most places. However, I think you may have to let that starboard chine loose and trim it just a little to get it to match the port one. It won't take much so don't go crazy there. It will probably take several small nib...